I think he's implying that Luxire doesn't execute pleats well.
I'm still not sure since I've had some come out very well and some not so well. I think the trouser fabric drape is a huge factor in whether they gape open or not (moreso than pleat depth). Honestly I'm currently on the fence about whether to keep trying with pleats for this reason.

I've been a customer for a number of years and have noticed the standard options have changed a number of times leading to unexpected results (granted mostly positive changes). It would be helpful if Luxire could maintain a page on the site that explains what standard options are used and keep it current.

Pretty sure Luxire was referring to a very specific scenario: "copy the provided garment but adjust the waist to 16" - the pattern created would match the original garment except the waist measurement would be different as requested.
If you just send a garment to be copied without any adjustments then the pattern should be an exact match to the garment.

Honestly I don't find the existing website that bad. Maybe not great for new customers but as a 'power user' I basically just use it to peruse fabrics (sort by price and page through until I find what I want). 99% of my interface with Luxire is through email or simply outlining details in the comment section of my order.

I measured some jeans I already had (Iron Heart 635s and Levis STF) and sort of took the average of the measurements. Luxire came back to me with a concern that one measurement would not work while using the selvedge but they were able to make a minor adjustment to make it work. They came out perfectly although the inseam strangely felt about 2" too long even though the measurements all checked out. I just adjusted on my second jeans order.